Contacts of the helix formed by residues 460 - 472 (chain A) in PDB entry 3DYQ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 460 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A MET* 4.2 12.6 - - + -
368A HIS* 3.7 27.7 + - + +
403A ILE* 3.7 26.0 - - + -
455A GLY 4.9 0.4 - - - +
456A PHE* 3.0 40.7 + - + +
459A PHE* 1.3 83.7 - - + +
461A LEU* 1.3 65.4 + - - +
462A ILE 3.7 0.2 - - - -
463A PRO* 3.6 2.5 - - - +
464A MET* 3.3 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 461 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A ILE* 3.1 47.8 - - + +
404A SER* 4.8 1.1 - - - -
406A GLU* 4.0 16.2 - - + +
407A VAL* 5.6 0.4 - - + +
456A PHE* 3.0 35.6 + - + +
457A ILE* 3.8 15.0 - - + +
460A VAL* 1.3 73.7 - - - +
462A ILE* 1.3 70.1 + - - +
464A MET* 3.2 2.5 + - - +
465A PHE* 3.0 50.2 + - + -
483A LEU* 3.9 27.8 - - + -
900A PCG 5.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 462 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A ILE* 2.9 41.5 + - + +
458A LYS* 4.1 9.2 - - - +
461A LEU* 1.3 72.8 - - - +
463A PRO* 1.3 66.9 - - + +
465A PHE* 3.1 1.2 + - - +
466A GLU* 2.7 56.8 + - + +
480A LEU* 3.9 8.8 - - + +
483A LEU* 4.1 15.3 - - + +
484A TRP* 3.6 33.9 - - + +
487A ARG* 4.0 15.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 463 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A MET* 4.5 7.2 - - + -
376A LYS* 6.3 2.0 - - - -
458A LYS 3.3 22.9 - - - +
459A PHE* 3.5 20.0 - - - +
460A VAL 3.6 9.2 - - - +
461A LEU 3.5 3.1 - - - -
462A ILE* 1.3 92.2 - - + +
464A MET* 1.3 64.2 + - - +
466A GLU* 3.2 23.8 + - - +
467A THR* 3.2 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 464 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A HIS* 3.9 18.2 - - + -
372A MET* 3.8 26.9 - - + +
396A ILE* 4.4 8.5 - - + +
399A LYS* 4.3 13.0 - - + +
400A CYS* 3.8 39.0 - - - +
403A ILE* 3.0 42.0 - - + -
460A VAL 3.3 14.3 + - - +
461A LEU* 3.2 10.8 + - + +
463A PRO* 1.3 78.8 - - - +
465A PHE* 1.3 65.3 + - + +
467A THR* 2.9 20.7 + - - +
468A VAL* 3.0 8.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 465 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A MET* 4.8 4.5 - - + -
400A CYS* 3.7 46.7 - - + -
404A SER* 4.7 2.2 - - - -
407A VAL* 4.0 18.2 - - + -
461A LEU* 3.0 46.5 + - + +
464A MET* 1.3 81.2 - - + +
466A GLU* 1.3 52.4 + - - +
467A THR 3.3 0.2 - - - -
468A VAL* 3.5 7.8 + - + +
469A THR* 2.7 37.9 + - - -
475A VAL* 4.1 19.5 - - + +
479A MET* 3.5 30.1 - - + -
480A LEU* 3.4 22.9 - - + -
483A LEU* 3.9 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 466 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A ILE* 2.7 39.3 + - + +
463A PRO* 3.4 15.6 - - - +
464A MET 3.1 0.2 - - - -
465A PHE* 1.3 76.7 - - - +
467A THR* 1.3 63.7 + - + +
469A THR* 3.3 14.3 + - - -
470A LYS* 3.5 14.7 + - - +
480A LEU* 4.1 19.9 - - + +
484A TRP* 5.2 4.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 467 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A MET* 3.9 11.5 - - + +
375A PHE* 4.0 24.9 - - - -
376A LYS* 4.2 32.5 - - + -
379A MET* 5.0 7.3 - - + +
396A ILE* 5.5 0.2 - - - +
463A PRO 3.7 10.7 + - - +
464A MET* 2.9 17.4 + - - +
466A GLU* 1.3 75.0 - - + +
468A VAL* 1.3 65.6 + - - +
469A THR 3.0 1.6 - - - -
470A LYS* 2.9 39.0 + - + +
471A LEU* 3.8 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 468 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A MET* 4.6 12.8 - - + -
375A PHE* 4.9 7.2 - - + -
393A LEU* 5.4 6.1 - - + -
396A ILE* 3.4 34.1 - - + -
397A LEU* 5.4 4.3 - - + -
400A CYS* 3.9 13.5 - - - -
464A MET 3.0 14.1 + - - +
465A PHE* 3.8 11.4 - - + +
466A GLU 3.4 0.2 - - - -
467A THR* 1.3 77.0 + - - +
469A THR* 1.3 58.3 + - - +
471A LEU* 3.0 11.8 + - - +
472A PHE* 3.0 35.1 + - + -
475A VAL* 4.0 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 469 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A PHE 2.7 21.3 + - - -
466A GLU 3.4 8.7 - - - -
467A THR 3.0 0.6 - - - -
468A VAL* 1.3 79.1 - - - +
470A LYS* 1.3 60.7 + - - +
472A PHE 3.2 21.4 - - - +
473A PRO* 3.2 23.3 - - + +
475A VAL* 3.3 17.2 - - - +
476A GLU* 3.8 23.9 + - + +
480A LEU* 3.5 13.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 470 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A MET* 4.5 22.2 - - + -
466A GLU* 3.5 14.6 + - - +
467A THR* 2.9 26.5 + - + +
469A THR* 1.3 79.0 - - - +
471A LEU* 1.3 61.0 + - + +
473A PRO* 5.1 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 471 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A PHE* 3.7 20.2 - - + -
379A MET* 3.4 37.0 - - + -
382A PHE* 4.2 19.5 - - + -
384A TYR* 3.5 24.1 + - + +
393A LEU* 4.1 22.4 - - + -
467A THR 3.8 1.5 + - - +
468A VAL* 3.0 10.3 + - - +
470A LYS* 1.3 83.6 - - + +
472A PHE* 1.3 76.3 + - + +
473A PRO* 3.7 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 472 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A CYS* 3.6 50.5 - - + -
273A LEU* 3.8 20.4 - - + -
276A LYS* 4.6 10.8 - - + -
277A PHE* 5.1 0.2 - + - -
384A TYR* 3.7 25.4 - + - -
393A LEU* 4.1 29.4 - - + -
397A LEU* 5.1 4.5 - - + -
468A VAL* 3.0 22.6 + - + +
469A THR* 3.2 9.2 - - - +
471A LEU* 1.3 93.9 - - + +
473A PRO* 1.3 62.5 - - - +
474A MET* 3.3 11.9 - - + -
475A VAL* 3.0 26.9 + - + +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il